obikmer/benchmark/downloads.sh

#!/usr/bin/env bash

set -euo pipefail

assemblies=(
    GCF_000005845.2
    GCF_000010245.2
    GCF_000007445.1
    GCF_000006665.1

    GCF_000006945.2
    GCF_000195995.1
    GCF_000009505.1
    GCF_000026565.1

    GCF_000016305.1
    GCF_000019965.1
    GCF_000240185.1
    GCF_000742135.1

    GCF_000069965.1
    GCF_000022565.1
    GCF_000306885.1
    GCF_003013715.1

    GCF_000009045.1
    GCF_000009825.1
    GCF_000022445.1
    GCF_000834255.1
)

SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
GENOMES_DIR="${SCRIPT_DIR}/run/genomes"

mkdir -p "${GENOMES_DIR}"

for acc in "${assemblies[@]}"; do
    echo "Downloading ${acc}"

    datasets download genome accession "${acc}" \
        --include genome \
        --filename "${acc}.zip"

    unzip -q "${acc}.zip" -d "${acc}"
    find "${acc}" -name "*.fna" |
        while read file; do
            obiconvert -Z ${file} >"${GENOMES_DIR}/$(basename ${file}).gz"
        done

    rm -rf "${acc}" "${acc}.zip"
done